It sounds like you may have a few things mixed up.
JSON is a way to represent data and is in no way specific to tiddlywiki. I believe that what you are referring to as JSON is the node version of tiddlywiki.
Are the pre-5.1.13 wiki single file html files? In what way will they not load? Would they load before?
I think that what you want to do is to split up all of your existing singe file tiddlywikis into .tid files and then share these files between separate wikis when running under nodejs, but that isn't very clear from what you are saying.